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- EMDB-55405: Catalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom... -

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Basic information

Entry
Database: EMDB / ID: EMD-55405
TitleCatalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom resolution.
Map data
Sample
  • Organelle or cellular component: catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water
KeywordsCatalase / NADPH / Protoporphyrin IX / OXIDOREDUCTASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
Biological speciesMicrococcus luteus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsLi J / Henderson R / Russo CJ / Wilson H / Chen S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
CitationJournal: To Be Published
Title: Comparison of human and bacterial monofunctional catalase structures obtained by electron cryomicroscopy.
Authors: Slowik D / Li J / Wilson H / Shtyrov A / Chen S / McMullan G / Russo CJ / Murshudov G / Henderson R
History
DepositionOct 17, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55405.png

Downloads & links

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Map

FileDownload / File: emd_55405.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.033486184 - 0.10773996
Average (Standard dev.)0.00004171449 (±0.0013882789)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 409.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55405_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55405_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55405_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : catalase with cofactor NADPH

EntireName: catalase with cofactor NADPH
Components
  • Organelle or cellular component: catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water

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Supramolecule #1: catalase with cofactor NADPH

SupramoleculeName: catalase with cofactor NADPH / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Micrococcus luteus (bacteria)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Catalase

MacromoleculeName: Catalase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: catalase
Source (natural)Organism: Micrococcus luteus (bacteria)
Molecular weightTheoretical: 58.09875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHSG EHQKTTPHAT GSTRQNGAPA VSDRQSLTVG SEGPIVLHDT HLLETHQHFN RMNIPERRPH AKGSGAFGEF EVTEDVSKY TKALVFQPGT KTETLLRFST VAGELGSPDT WRDVRGFALR FYTEEGNYDL VGNNTPIFFL RDPMKFTHFI R SQKRLPDS ...String:
HHHHHHHHSG EHQKTTPHAT GSTRQNGAPA VSDRQSLTVG SEGPIVLHDT HLLETHQHFN RMNIPERRPH AKGSGAFGEF EVTEDVSKY TKALVFQPGT KTETLLRFST VAGELGSPDT WRDVRGFALR FYTEEGNYDL VGNNTPIFFL RDPMKFTHFI R SQKRLPDS GLRDATMQWD FWTNNPESAH QVTYLMGPRG LPRTWREMNG YGSHTYLWVN AQGEKHWVKY HFISQQGVHN LS NDEATKI AGENADFHRQ DLFESIAKGD HPKWDLYIQA IPYEEGKTYR FNPFDLTKTI SQKDYPRIKV GTLTLNRNPE NHF AQIESA AFSPSNTVPG IGLSPDRMLL GRAFAYHDAQ LYRVGAHVNQ LPVNRPKNAV HNYAFEGQMW YDHTGDRSTY VPNS NGDSW SDETGPVDDG WEADGTLTRE AQALRADDDD FGQAGTLVRE VFSDQERDDF VETVAGALKG VRQDVQARAF EYWKN VDAT IGQRIEDEVK RHEGDGIPGV EAGGEARM

UniProtKB: Catalase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 422 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
154.0 mMNaClsodium chloride
10.0 mMNaH2PO4-Na2HPO4sodium phosphate
0.2 mMC21H30N7O1P3Nicotinamide adenine diphosphate
5.0 mMC32H58N2O8SCHAPSO
GridModel: HexAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 45 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.1 mrad
DetailsOnly one optical group, with minimal beam tilt.
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 27182 / Average exposure time: 3.0 sec. / Average electron dose: 50.4 e/Å2
Details: Images collected with AFIS with maximum image shift of 1.5 microns.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 18.1 µm / Calibrated defocus min: 11.4 µm / Calibrated magnification: 273437 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 18.1 µm / Nominal defocus min: 11.4 µm / Nominal magnification: 155000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1046104
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Startup map was from a parallel catalase structure from Agrobacterium radiobacter from the same publication.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Details: Standard Relion gold standard. / Number images used: 261172
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 65293 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1gze


Chain - Chain ID: A / Chain - Residue range: 7-505 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: The initial model was PDB entry 1GWE.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9t0m:
Catalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom resolution.

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